Hi Jake & Diego,
Maybe a very small modification to ace() could help to accomodate some of these
issues. Currently, ace(type = "discrete") checks the branch lengths of the tree
and throws an error if any of them is zero or negative. I think zero-length
branches could be allowed. This seems quite reasonable since matrix exponential
works as expected in this situation, e.g., with expm:
R> expm::expm(matrix(rep(0, 4), 2, 2))
[,1] [,2]
[1,] 1 0
[2,] 0 1
I'm not sure why the current check rejects trees with zero-length branches
(probably there was a good reason some time ago). If this is changed, then
calling ace() with a tree modified with multi2di() will be easier since the
last function adds zero-length branch(es) in the tree.
Best,
Emmanuel
----- Le 15 Sep 21, à 21:33, Jacob Berv jakeberv.r.sig.ph...@gmail.com a écrit :
> Hi Diego,
>
> If your tree has polytomies and the branches have no length information, I am
> not sure if likelihood model-based reconstruction is right.
>
> The ace function (and all other similar functions based on likelihood) will
> assume that your branch lengths represent some kind biological information
> (usually time), and the degree to which characters evolve will be related to
> the branch length. I therefore might prefer parsimony in this situation to get
> a general sense of what is going on.
>
> As an experiment, you could assign all branches to be equal (e.g. = 1), but
> then
> you are imposing this assumption on the analysis. In order to evaluate the
> effects of this assumption, and if you are specifically interested in
> reconstructing the ancestral states for a particular node, you could generate
> a
> few sets of simulated branch lengths (which you could then pass to ace), to
> see
> if the reconstruction is robust to a range of variation in branch lengths. You
> could also replicate using multi2di to see how robust your reconstruction is
> to
> alternative resolutions.
>
> Best,
> Jake
>
>
>> On Sep 15, 2021, at 2:16 AM, Diego Almeida-Silva
>> <silva.diego.alme...@gmail.com>
>> wrote:
>>
>> Dear colleagues,
>>
>> I am trying to estimate ancestral states for two binary characters in a
>> full morphology-based phylogenetic tree. I am using ace function,
>> type="discrete" and kappa=0 as arguments. Unfortunately, I am dealing with
>> two problems about this issue: my topology have three polytomies and tree
>> branches have no lengths.
>>
>> To perform ancestral state estimation, I firstly used the multi2di
>> function. However, this procedure creates artificial nodes in the topology.
>> This becomes a new problem, since states at these new nodes are also being
>> estimated.
>>
>> Is there another way to deal with this situation? There are functions (or
>> packages) other than those of phytools that are able to deal with
>> polytomies and the absence of branch lengths in ancestral state
>> reconstruction?
>>
>> Thanks in advance!
>> Diego
>>
>> [[alternative HTML version deleted]]
>>
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